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- PDB-3ugu: Crystal Structure of p44 (Splice Variant of Visual Arrestin) -

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Basic information

Entry
Database: PDB / ID: 3ugu
TitleCrystal Structure of p44 (Splice Variant of Visual Arrestin)
ComponentsS-arrestin
KeywordsSIGNALING PROTEIN / arrestin fold / signal termination / GPCR / outer segment
Function / homology
Function and homology information


opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane ...opsin binding / Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / G protein-coupled receptor binding / phosphoprotein binding / signal transduction / membrane / identical protein binding / cytosol
Similarity search - Function
Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBatra-Safferling, R. / Granzin, J.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structure of p44, a Constitutively Active Splice Variant of Visual Arrestin.
Authors: Granzin, J. / Cousin, A. / Weirauch, M. / Schlesinger, R. / Buldt, G. / Batra-Safferling, R.
History
DepositionNov 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Structure summary
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-arrestin


Theoretical massNumber of molelcules
Total (without water)42,4181
Polymers42,4181
Non-polymers00
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.964, 71.583, 79.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein S-arrestin / 48 kDa protein / Retinal S-antigen / S-AG / Rod photoreceptor arrestin / S-arrestin short form


Mass: 42417.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: SAG / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08168
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CORRESPONDS TO S-ARRESTIN, ISOFORM B. THE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE ...THE SEQUENCE CORRESPONDS TO S-ARRESTIN, ISOFORM B. THE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE CANONICAL SEQUENCE BY HAVING ALA AT POSITION 370.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14% PEG 4000, 0.1M MES, 50 mM KH2PO4, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.85→41.68 Å / Num. all: 33085 / Num. obs: 33085 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 19.68 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1559 / % possible all: 96.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.482 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1674 5.07 %RANDOM
Rwork0.1743 ---
all0.1763 33085 --
obs0.1763 33035 99.04 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.542 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5199 Å20 Å2-0 Å2
2--0.9303 Å2-0 Å2
3----1.4502 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 0 402 3079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062764
X-RAY DIFFRACTIONf_angle_d1.0753759
X-RAY DIFFRACTIONf_dihedral_angle_d12.6921040
X-RAY DIFFRACTIONf_chiral_restr0.075447
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90440.28511350.22432507X-RAY DIFFRACTION97
1.9044-1.96590.23711410.1732600X-RAY DIFFRACTION100
1.9659-2.03610.19881590.16662590X-RAY DIFFRACTION100
2.0361-2.11770.21181300.16012575X-RAY DIFFRACTION99
2.1177-2.2140.20251580.16772586X-RAY DIFFRACTION100
2.214-2.33070.20871190.17412646X-RAY DIFFRACTION100
2.3307-2.47670.20741380.17852619X-RAY DIFFRACTION100
2.4767-2.66790.25061330.19752637X-RAY DIFFRACTION100
2.6679-2.93620.27241400.19192632X-RAY DIFFRACTION100
2.9362-3.36070.21511580.17462640X-RAY DIFFRACTION99
3.3607-4.23280.18181310.16132656X-RAY DIFFRACTION98
4.2328-33.48770.19641320.16682673X-RAY DIFFRACTION95

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